Getting started

To enable the Bioconductor style in your R Markdown vignette you need to include the following in the DESCRIPTION file:

VignetteBuilder: knitr
Suggests: BiocStyle, knitr, rmarkdown

Style macros

BiocStyle introduces the following macros for referring to R packages:

IRanges, for Bioconductor software, annotation and experiment data packages,
data.table, for R packages available on CRAN,
rmarkdown, for R packages available on GitHub,
MyPkg, for R packages that are not available on Bioconductor, CRAN or GitHub.

Figures

Assign captions to figures in the code chunk option fig.cap to automatically number them, and to be able to reference them, see Figure @ref(fig:plot). The figure label is generated from the code chunk label by prefixing it with fig:.

Regular figure. The first sentence of the figure caption is automatically emphasized to serve as figure title.

Small and wide figures can be specified by fig.small and fig.wide code chunk options.

Small figure. A plot produced by a code chunk with option fig.small = TRUE.

Wide figure. A plot produced by a code chunk with option fig.wide = TRUE.

Equations

To number and reference equations, put them in equation environments and assign labels to them, see Equation @ref(eq:binom).

\[\begin{equation} f\left(k\right) = \binom{n}{k} p^k\left(1-p\right)^{n-k} (\#eq:binom) \end{equation}\]

Tables

Like figures, tables with captions will also be numbered and can be referenced, see Table @ref(tab:table).

(#tab:table) A simple table. With caption.
Fruit	Price
bananas	1.2
apples	1.0
oranges	2.5

Cross-references

Apart from referencing figures (Section @ref(figures)), tables (Section @ref(tables)), and equations (Section @ref(equations)), you can also use the same syntax to refer to sections by their default labels generated by pandoc.

Side notes

Footnotes are displayed as side notes on the right margin¹, which has the advantage that they appear close to the place where they are defined.

some thoughts

library(ProjectAsPkg)
library(randomForest)

## randomForest 4.6-14

## Type rfNews() to see new features/changes/bug fixes.

features = get_features()
targets = get_targets()
rf = randomForest(features, as.numeric(targets$gene_expression), ntree=10)

plot(targets$gene_expression, predict(rf, features))

print(varImpPlot(rf))

##          IncNodePurity
## Control       2401.999
## Dnase        20615.884
## H2az          3850.427
## H3k27ac      13641.846
## H3k27me3      3453.441
## H3k36me3     17122.410
## H3k4me1       2800.139
## H3k4me2      21710.998
## H3k4me3       6703.127
## H3k79me2     48711.869
## H3k9ac       16451.232
## H3k9me1       2944.674
## H3k9me3       2573.372
## H4k20me1      2867.282

Session info

## R version 3.5.0 (2018-04-23)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 16.04.4 LTS
## 
## Matrix products: default
## BLAS: /usr/local/lib/R/lib/libRblas.so
## LAPACK: /usr/local/lib/R/lib/libRlapack.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] randomForest_4.6-14 ProjectAsPkg_0.1.0  BiocStyle_2.8.0    
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_0.12.16     rstudioapi_0.7   knitr_1.20       xml2_1.2.0      
##  [5] magrittr_1.5     roxygen2_6.1.0   MASS_7.3-50      R6_2.2.2        
##  [9] rlang_0.2.0      highr_0.6        stringr_1.3.1    tools_3.5.0     
## [13] xfun_0.1         htmltools_0.3.6  commonmark_1.6   yaml_2.1.19     
## [17] rprojroot_1.3-2  digest_0.6.15    assertthat_0.2.0 bookdown_0.7    
## [21] pkgdown_1.1.0    crayon_1.3.4     fs_1.2.6         memoise_1.1.0   
## [25] evaluate_0.10.1  rmarkdown_1.9    stringi_1.2.2    compiler_3.5.0  
## [29] desc_1.2.0       backports_1.1.2

this is a side note entered as a footnote↩

Example Vignette

Sean Davis